Well, I have been looking around on the web for a bit and figured I should just post to my blog. We are in the market for a used Roche GS FLX sequencer. Anyone know of one for sale? We had planned to buy a new one but with the 3rd generation sequencers coming out soon it seems unwise to spend 500K on a new machine. But I like the current capabilities in the Roche GS FLX, as well as the apparently soon to be released ~1000 base pair reads. So we still would like to have the technology here at UC Davis. So if you know of one for sale, please let me know.

Sunday, March 28, 2010

I am teaching a class this spring and as part of the class am having one lecture on "Phylogenetic trees and methods." I would like to link to (and be able to mix and match material from) some review paper on this topic. So I am searching for something that is Open Access and preferably with a broad Creative Commons license. Anyone know of anything good?

Monday, March 22, 2010

Just heard an ad on the radio from the Vote Yes on Proposition 16 campaign here in California. And got a heads up from a friend about it too. Just to cut to the chase before getting into detail - this initiative is horrendous and deceptive. Here are some details

3. Not surprisingly, many other utilities have come out against this, as it clearly favors PG&E, aka the status quo. I am not overly sympathetic to the opinions of these other utilities but it seems that the initiative is more about reducing competition than in favoring democracy.

4. One thing that really annoys me is the component of the proposition that a two-thirds majority vote will be required before local communities can change their energy plans. To then say that this initiative is about protecting our right to vote is just absolutely offensive. What this is a way to try and make change of any kind very very difficult. In this day and age, with energy becoming more and more of an issue, we should have as much flexibility as possible. What we do not need is an initiative that requires a 2/3 majority to make changes.

5. The most astonishing aspect of the proposal has been some of the words from the head of PG&E, as reported in the Mercury News

Asked why the company was sponsoring the initiative, Darbee referred to the 2006 battle in which it spent more than $11 million to prevent Davis, Woodland and West Sacramento from defecting to the Sacramento Municipal Utility District.

"So it was really a decision about could we greatly diminish this kind of activity for all going forward rather than spending $10 (million) to $15 million a year of your money to invest in this," Darbee told the shareholders. "The answer was yes."

So basically this is there way to limit the choices of cities by putting this on a statewide ballot. In essence, whether liberal or conservative, Democrat or Republican, I can't see why anyone would support this Proposition. A conservative could easily see this as PG&E trying to be the big hand of government to take away taxpayer choice. A liberal could see this as a company using their money to buy votes and prevent choice in energy usage. I really cannot see any potential upside in this for anyone but PG&E. Lovely

Simple solution. Vote No on Proposition 16. More comprehensive solution would be to actually punish PG&E for the audacity and idiocy of this measure as well as the misleading nature of all of their ads and claims about it. Not sure how to do that but boy do they deserve it.

The public comment period begins at 8:30 a.m., Wednesday March 24. Following that 40-minute period, President Mark Yudof, Regents Chairman Russell Gould, Interim Provost Lawrence Pitts, Senior Policy Advisor Christopher Edley and select chancellors will discuss the recent events and the actions they are taking to ensure that these types of incidents do not occur in the future.

The first uses seem to be in and around 2001. See this article from Nature Reviews Genetics in 2001 Mining the bibliome. And another one with a very similar title in EMBO in 2002: Mining the Bibliome (with some other words in the title). And another one in Pharmacogenomics entitled Mining the bibliome.

From the abstract: "The definition of transcriptional networks through measurements of changes in gene expression profiles and mapping of transcription factor binding sites is limited by the moderate overlap between binding and gene expression changes and the inability to directly measure global nuclear transcription (coined “transactome”)."

I have no real clue what that means.

I confess, going to skip this paper. So I will not figure out if there is some clearer meaning. But here's a guess - the word is unnecessary.

"The sequence and nature of all the protein amino-termini (N-termini) within the proteome (the N-terminome) provides valuable functional annotation, since translation start sites, N-terminal isoforms, modifications and truncations determine the cellular localization, activity and fate of most proteins"

Just got pointed to a fun paper from 2002 "A Crisis in Postgenomic Nomenclature by Stanley Fields and Mark Johnston" by Mark Johnston himself. Their paper, in Science, is available for free on Stanley Fields website here. It is actually a hilarious tongue in cheek read where they proceed from arguing for more specificity in omics names (e.g., they go so far as to propose a EC# like system with things such as the "4.7.5.3.8ome" and also that conditions should be specified like the "37°-7.4-G1-Golgi-N-but-not- 63O-linked glycosylome". And they end with a proposal to replace the term "the cell" with either the someone or the omesome. It is definitely worth a read.

Given that there were only 847 google hits as of today, the word clearly has not taken off, which is good. But alas it is still being used, even in titles. As far as I can tell, what they mean by the term is "All the miRNAs in a particular cancer class" --- unclear to me why that needs an ome.

On the web site the seem to define this project as an attempt to "collect variation causing disease (mutations) in all genes world wide" so I guess that is what variome means to them. So - I wonder here - what is wrong with "polymorphisms"??????

HT to @ivanoransky and @boraz for pointing this out to me (by feeding my other people's tweets).